


Mass Effect: Biotic Soldier

by Cereith



Category: Mass Effect
Genre: Alternate Universe - Canon Divergence, Angst, I'm talking painfully slow here people, It will cover both games, Kai Leng does not exist, LIKE A LOT OF ANGST, M/M, ME2 and ME3, Slow Build, Slow Burn, post-ME3
Language: English
Status: In-Progress
Published: 2015-07-23
Updated: 2015-10-11
Packaged: 2018-04-10 19:49:27
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 2
Words: 4,387
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4405190
Author URL: https://archiveofourown.org/users/Cereith/pseuds/Cereith
Summary: <blockquote class="userstuff">
              <p>Prompt:<br/>"AU where Cerberus pulls a Winter Soldier and Kai Leng is actually Kaidan that Shepard left on Virmire."</p><p>Commander John Shepard decided to save Ashley instead of Kaidan on Virmire. Kaiden survives, but is extremely weakened from the bombs blast making him an easy target for Cerberus to capture and turn him into their puppet.</p><p>Shepard broken-heartily remembers the times he spent with Kaidan as he continues to live and his friend does not. He recalls the times they spent with each other at BAaT, when they enlisted together, and as they served together.</p>
            </blockquote>





	1. The Choice

**Author's Note:**

> This fic was enabled, i mean encouraged by ArchLucie!!
> 
> Well just like the prompt says, Kaiden is Kai Leng, except not really because in they fic Kaid Leng does not exist.  
> Its an interesting twist. I hope you all like it!!
> 
> Enjoy!  
> :)
> 
> P.S.  
> The prompt was not created by me

**Shepard on Virmire before the bomb detonates**

 

“Go get Ashley and get out of here Commander!” Kaidan’s voice was heard over the comms as he fought off incoming Geth. Surrounding him like a pack of wild dogs.

 

“Commander, get the Lieutenant and go!” Ashley was heard this time as she activated the bomb that would destroy Saren’s base on Virmire.

 

He had to decide. He had to choose who lived and who died that very second. In that moment Commander Shepard wished it wasn’t him that had to make this choice, to choose between two people closest to you, but he wouldn’t wish this decision on anyone else either. So he made a choice, one that would follow him for as long as he lived.

 

“Williams, radio Joker and tell him to meet us near the bomb site.” Shepard’s firm voice held the tinge of burden from his choice.

 

“I-“ Ashley tiredly breathed. “Yes, Commander.”

 

“It’s the right choice and you know it Ash.” Kaidan, ever so self-sacrificing, willing to die for his comrades if it meant they’d be saved.

 

How long has it been since the bomb was activated? If he was quick enough maybe he could save them both and this choice would have been meaningless.

 

“Alenko, hold tight.” Instead of worry in his voice now he had a bit of hope. “I’m going to get you!”

 

“Yeah,” Kaidan did not sound as hopeful. “We both know that’s not happening Commander.”

 

Shepard ran as fast as he could back to the bombsite. He had to be quick, he needed to get Williams to safety and go get Alenko before time ran out. He had to try! He had to! Damn it why couldn’t he believe he could do it himself!

 

He made it to the bombsite as Saren descended upon them. Shepard fired off several shots at the Spectre, but the Turians biotic filed stopped all of his projectiles. Shepard took cover as Saren tried to convince him that the Reapers were a godsend. That organics should submit to them in order to live a better life. He did not have time for this!

 

Moments later, Shepard was unsuccessful in convincing the Turian to turn himself in to the Council. Saren escaped to his ship as the Normandy made it to the bombsite to extract them. Shepard helped Ashley get to the safety of the Normandy. He turned around and made to exit the ship, but the hatch door was closing.

 

“Joker, open the hatch door. I need to go get Alenko!” Shepard yelled over the comms to the Normandy’s pilot.

 

“Negative Commander. The bomb is almost out of time we have to haul ass out of here!” The Normandy shook as it left the atmosphere of the planet. A moment later the blast from the bomb was seen from a safe distance in space.

 

Shepard looked at the planet below, where his Lieutenant had just been blown to bits all because he wasn’t fast enough.

 

“Damn it!” Shepard beat his fist against the console in front of him. The door to the observation deck opened as someone stepped inside. Shepard turned around to see Ashley slowly walking up to him.

 

“Williams, I’m-“ Shepard jerked his head as Ashley brutally slapped him across the face. The sound of skin hitting skin echoed in the room. He rubbed his hand on his now aching cheek.

 

“Why did you pick me?” She hissed out. Her body was tense like she was struggling to keep herself in check.

 

“I tried to-“ Ashley lifted her fists to beat against his chest.

 

“To what? Huh!” Tears started to stream down her face as she kept hitting Shepard, “It should have been me!”

 

Shepard didn’t budge, he stood there and let Ashley vent as she hit him. Her blows couldn’t compare to the pain of his aching heart. A hole torn into it that can never be filled. His own tears began to stream down his face.

 

“You should have saved him!” She roared.

 

“I wanted to save you both!” He shouted back, catching her by the wrists as she lifted her fists again.

 

She easily freed herself from his grasp; he moved forward and embraced her. Ashley hugged his back as they both wept for their lost friend.

 

“He was my friend,” his voice was hoarse and tired. “I wanted to save him too.”

 

They grieved their friend in sob filled silence as the Normandy glided away from Kaidan Alenko’s final resting place.

 

The Normandy and her crew where long gone by the time Cerberus ships arrived to investigate their friend’s grave.

 

_-_

 

**Kaidan on Virmire before the bomb detonates**

 

“Yeah,” Kaidan knew his Commander was trying to give him hope, but they just didn’t have enough time. “We both know that’s not happening Commander.” The comms cut out.

 

He took cover behind one of the large metal containers while Geth surrounded him at every turn. He shot off several rounds to the head of the Geth closing in on him then used a biotic Throw to push back the others. He was drastically down to one thermal clip as he went back into cover. Kaidan would need to rely heavily on his biotics. Quickly going out of cover he blasted off a Singularity at the two closest Geth. He aimed then shot off a round that pierced both heads of the synthetics. Then Kaidan used a Slam to pin down three Geth simultaneously and shot each in its robotic eye socket next a Shockwave to the four incoming behind them knocking them off the cliff-side of the building.

 

Kaidan fought them off as best he could but there were just too many as more kept coming and coming.

 

He was also running out of time, the bomb would go off any second. Kaidan urgently needed to find a way to survive the blast.

 

He strapped on his helmet and activated the breather settings then ran towards the cliff-side of the building and dived into the water below. Using his biotics he dove deeper and deeper into the water.

Up above him the bomb detonated, spreading its scorching heat over the whole land. Destroying the any Geth and any remnants of life left on the base.

 

To further protect himself Kaidan rapidly encased himself in a powerful biotic field, staving off the shockwave from the blast, however it did little as it only pushed him further out to sea.

 

Once he was far enough away Kaidan ascended up the water, feeling exhausted and worn from the heavy use of his biotics. He drifted in the water until he reached a beach. With what little strength he had Kaidan hefted himself up the beach to get away from the waves of the water.

 

Moments later Kaidan saw several figures approaching him, all armed. He lifted his weapon, but could not properly aim as his vision blurred. His whole body felt heavy and tired. Kaidan dropped his hand and weapon to the sand.

 

He slowly lost consciousness.

 

_-_

 

**Shepard after saving the Citadel and the Council**

 

Shepard had saved the galaxy from an impending enemy. He defeated Saren and destroyed Sovereign.

 

The Normandy and her crew saved the Citadel as well as its Council.

 

Kaidan would have been proud.

 

_-_

 

**Shepard after the Normandy is destroyed**

 

He managed to convince Williams to get to the escape pods and saved the Normandy’s pilot.

 

Shepard is helplessly drifting out into the cold void of space as his suit drastically leaks out his precious oxygen supply.

 

In his final moments of consciousness he felt content that he would be able to see, his beloved friend, Kaidan Alenko in the afterlife.

 

 


	2. Denial

**Summary for the Chapter:**

> Shepard and Kaidan meet for the first time.  
> AND  
> Shepard is brought back to life by Cerberus and finds out what's been happening for the past two years.

**Notes for the Chapter:**

> I'm sorry this took so long to continue. I haven't really figured out the direction of this fic when i posted the first chapter. I spent the last few months figuring out major plot points and story developments. Now i believe i have a more solid and defined idea of where this fic is going.  
> Again, i am sorry this took so long, I'm hoping the next chapter will be posted a lot sooner than this one.  
> That being said, i hope you enjoy this chapter.
> 
> :)

It's been a long day without you, my friend

And I'll tell you all about it when I see you again

We've come a long way from where we began

Oh, I'll tell you all about it when I see you again

When I see you again

**-See You Again, Charlie Puth**

 

_-_

 

**Shepard awaiting to depart to BAaT**

_He sat on the stone cold bench waiting for the shuttle that would take him to Biotics Acclimation and Temperance Training, BAaT. At least that’s what they called it. Anderson, his adoptive father, said it would be a good idea to go since no one on Earth really knew what they were doing and they didn’t want to ask for help from the Asari, because it would make humanity look weak or something like that._

_The metal creaked as ships on other docking bays landed to let off passengers or let on new ones. On one of the ships he saw a family of three get off, a mom, a father, and a teenage boy that looked around his age. The family were slowly walking towards his docking bay with a look of foreboding on their faces. They stopped in front of the security guards keeping watch over the bays entrance. Both parents seemed to be pleading with the guards, but the guards only shook their heads; denying what the parents had wanted. Accepting this, both parents leaned down to hug their son and whisper reassurances in the teens ear. The boy nodded to his parents then turned to walk into the bay as the guards granted him entrance._

_As they boy walked tentatively into the bay, he could now see the teenager better. The boy had raven black hair and a black duffel bag slung over his shoulder. He wore a casual gray cotton jacket, blue t-shirt, and blue faded jeans. The boy looked for somewhere to sit, but all the other benches or areas where someone could sit were already occupied. The boy looked over at his direction, honey colored eyes were silently asking if he could sit next to him. He was the only one siting on the bench so he moved to the side to allow the boy to sit next to him. The teen quickly walked up to take a seat before someone else could snag it from him._

_They sat in silence, neither of them starting a conversation. The boy looked over to his parents on the other side of the glass; he could see Anderson on the other side too. Anderson walked up the boy’s parents and started talking with them as they all waited for their respected teens to depart._

_The raven haired boy fidgeted nervously in his seat and kept moving his hands like he didn’t know what to do with them. He understood the teens worry. The teen was about to leave his family to go to some unknown off world training facility. He didn’t want to leave Anderson either, but he knew he had to go. He figured he might as well try and offer the boy a friendly hand._

_“Are those your parents?” He asked softly so as not to startled the teen while he’s on edge._

_“Yeah,” The teen said quietly. He turned his head to look at him shyly. “Are yours here too.”_

_“The guy talking with your parents is Anderson. He’s my adoptive father, but I still like calling him Pops. He says it make him feel old, although I know he likes it.” He chuckled lightly making the teen lose some of the tension he had._

_“My names John Shepard, but you can just call me Shepard.” He extended a hand to the teen boy._

_“Kaidan Alenko,” They shook hands and Kaidan fell into a more relaxed state._

_“I don’t mean to pry, but I couldn’t help noticing you were a bit nervous earlier.”_

_“Uh, yeah,” Kaidan exhaled a breath, “I am a bit jittery, but its like one of those first times kind of jitters, you know.”_

_He nodded in understanding, “Is it your first time off planet?”_

_“Yeah, you?” Kaidan asked curiously._

_“I’ve been in space before.”_

_“Really?”_

_“Yeah, Anderson is in the Alliance and he’s almost always on an Alliance ship so he takes me with him instead of leaving me on Earth.” Shepard looked over at Anderson. The man really did change his life by taking him out of the orphanage he grew up in and raising him from age eight. Anderson really was like a father to him._

_“My dad is in the Alliance too.” Kaidan said looking over to his father then back at Shepard. “I’ve never went with him on Alliance business before though. I always stayed on Earth with my mom.”_

_“How is it up there?” Kaidan asked after a moment of silence. “You know in space.”_

_“It’s spacey,” Kaidan snorted at that. Shepard thought for a bit on how to describe his view on space. “It’s hard to put into words. It’s big sure, but its also kind of beautiful with all the different planets and stars up there and all the different kinds of life it has.”_

_“Guess I won’t know until I see it.”_

_“I think you’ll like it.” Shepard offered a smile to Kaidan._

_“Yeah?” Kaidan returned the sentiment._

_“Yeah,” Shepard clapped him on the shoulder, “it’ll be like a space adventure.”_

_Kaidan laughed at that causing him to laugh as well. Once the shuttle arrived they both waved farewell to their respective families._

_The two set off on their first, of many, adventure as friends._

 

_-_

 

**Shepard escaping the Cerberus Base and meeting the Illusive Man**

 

Once again he was thrown back into the fray.

 

The last thing he expected was to wake up in a Cerberus hospital facility being under attack by their own mechs in order to kill him while he was recovering. Why was he recovering to begin with? He was sure he was as good as dead when the Normandy was attacked, yet here he is.

 

He fought his way through the Cerberus facility with Miranda’s voice guiding him. Deeper into the facility he encountered a man fighting off mechs. Once the mechs were destroyed the man, Jacob Taylor, explained to him the situation of what was going on.

 

His death, the destruction of the Normandy, his crew, everything.

 

Jacob led the way through the Cerberus base, before Wilson commed saying he was under attack. Once they got him out of trouble the three proceeded to advance further to get to the shuttles and escape. When they neared the shuttles a woman with pale skin and raven black hair stepped out, shooting Wilson on sight.

 

Miranda was unfazed by Shepard pointing a gun at her. She just calmly explained that Wilson was the one aiming to kill Shepard in his weakened state. Once things settled the three headed escaped on the Cerberus shuttle. On the shuttle Miranda mentioned that he would have to answer a few questions before he meets the Illusive Man.

 

“Come on Miranda more tests? Shepard took down those mechs without any trouble. That has to be good enough.” Jacob said.

 

“Its been two years since the attack. The Illusive Man needs to know Shepard’s personality and memories are intact. Ask the questions.” Miranda was apparently skeptical of Shepard.

 

“Did you say two years? I’ve been gone that long.” To say he was shocked would be an understatement though he didn’t show it.

 

“Two years and twelve days. And you were on an operating table for most of it.” Jacob clarified.

 

Two years.

 

He’s been considered dead for two years and somehow they brought him back to life.

 

“The sooner we start; the sooner we can be done. Start with personal history.” Miranda said sternly.

 

“Ok,” Jacob brought up his Omni-Tool to read of the info Shepard, “Records say you grew up on Earth in a tough environment. Until you were adopted by a David Anderson. Do you remember him?”

 

“Yeah, I do.” How could he forget one his closest friends and family? “After saving the Council from Sovereign they asked for my recommendation on selecting someone to be the first Human Councilor. I choose Anderson over Udina.”

 

“Councilor Anderson’s efforts on asserting Humanities place in the Galaxy are steadily increasing with the help of his Advisor, Udina.” Miranda said. Something about it made Shepard proud of his father. He briefly wondered what Anderson had been up recently until Jacob interrupted his thoughts with the next question.

 

“When you grew older you enlisted and survived a thresher maw attack that wiped out the rest of your team. Do you remember that?”

 

“I lost a lot of friends that day. Going through something like that changes you, it can break you. If you let it.” He made peace with what happened that day. He learned from what happened and used that knowledge to prevent other such situations from happening again.

 

“I read the report. Fifty marines died on Akuze. You were the only one who lived.” Jacob said sadly then turned to Miranda and said, “Satisfied Miranda?”

 

“Almost.” Surprisingly she wasn’t completely satisfied. “Let’s try something more recent.”

 

She took a moment to gather her thoughts before proceeding.

 

“Virmire,” _No please anything but that!_ “Where you destroyed Saren’s cloning facility. You had to leave one of your squard behind to die in the blast.”

 

Shepard clenched his fist to try an alleviate the growing pain within him.

 

“Lieutenant,” _Please don’t say his name!_ “Kaidan Alenko was killed in action. It was your call. Why did you leave him behind?”

 

Every word sent a dagger straight through his heart. The guilt, sorrow, and rage all threatening to spill out of him at once at remembering what he did and what he didn’t allow himself to process. He clenched his fists tighter, trying to push away his guilt and… _his_ death. He couldn’t deal with that right now, he just couldn’t or he’ll break.

 

It felt like an eternity when in reality it was a mere second before he spoke with one calming breath.

 

“I left a friend to die that day, and I didn’t do it casually.” Tears threated to come out, but he pushed them back, pushed it all away. “But I had to save as many people as I could.”

 

“Kaidan,” Just saying his name almost made his heart shatter to pieces. “gave his life for the rest of the team. Without him I couldn’t have stopped Saren. He died a hero.” _A better one that I could ever be._

 

“I understand, Commander.” Jacob said. “And I wasn’t judging your decision. Everybody at Cerberus knows that cloning facility had to be destroyed.”

 

“Your memory seems solid. There are other tests we really should run-“

 

“Come one Miranda.” Jacob interrupted. “Enough with the quizzes. The memories are there, and i can vouch for Shepard’s combat skills personally.”

 

“I suppose your right.” Did this woman just see him as some sort of lab rat? “We’ll have to hope the Illusive Man accepts are little field test as evidence enough.”

 

They fell into silence as they continued their voyage to meet the Illusive Man.

 

_-_

 

“The Illusive Man is waiting for you in the other room.” Miranda called over her shoulder as she peered down at her console.

 

Not even a second to breath and they already want him getting down to business after docking. Shepard followed the small hallway and down the stairs. He stood in the middle of a blue ring on the floor as he was being scanned by the room tech.

 

 A virtual image of himself appeared in a completely different room. In front of him was a man holding a cigar while siting upon his ‘throne’. Behind the man was an orange sun with hues of blue outlining it.

 

“Commander Shepard.” The Illusive Man said.

 

“Illusive Man,” Shepard crossed his arm defiantly. “I though we’d be meeting face to face.”

 

“A necessary precaution. Not unusual for people who know what you and I know.” The Illusive Man said smugly.

 

“You might be the reason I’m still alive, but that doesn’t mean I trust you.” He didn’t ask to be brought back to life. He didn’t owe this arrogant bastard anything.

 

“You need to put your personal feeling aside. Humanity is up against the greatest threat of our brief existence.”

 

“The Reapers.”

 

“Good to see your memory’s still intact. How are you feeling?” Like this man cared about how he was actually feeling.

 

“You need to earn the right to ask me those kinds of questions.” Shepard wasn’t about to give the Illusive Man anything regarding himself.

 

“Cerberus isn’t as evil as you believe. You and I are on the same side; we just have different methods.”

 

Seriously? He wasn’t about to get into a moral debate with him.

 

“Cut to the chase. What are the Reapers doing that made you decide to bring me back.”

 

“We’re at war,” The Illusive Man stood and walked over to the virtual image of Shepard. “No one wants to admit it, but humanity is under attack. While you’ve been sleeping, entire colonies have been disappearing. Human colonies.”

 

“We believe its someone working with the Reapers.” He continued. “Just as Saren and the Geth aided Sovereign. You’ve seen it yourself. You bested all of them. That’s just one reason we choose you.”

 

Shepard asked about Cerberus’ involvement in a war, the Reapers only abduction humans, and the status on Alliance Aid to help the disappearing colonies. Though he had one more thing nagging at him.

 

“You could have trained an entire army for what you spent to bring me back.”

 

“Your unique. Not just in ability or what you’ve experienced but in what you represent. You stood for humanity at a key moment. You’re more than a solider- You’re a symbol. And I don’t know if the Reapers understand fear, but you killed one. They have to respect that.”

 

Words never rang more hollow to him. He was a capable soldier sure, but a symbol? No, he wasn’t a symbol. He’s just one man, one man who happened to step up when it was needed for him to. Anyone else, anyone with his belief would have done the same.

 

“If what you say is true, if the Reapers are behind this, I’d consider helping you.” He needed something, some form of physical proof.

 

“I’d be disappointed if you accepted any of this without seeing for yourself. I have a shuttle ready for to take you to Freedom’s Progress, the latest colony to be abducted.” The Illusive Man went and sat back down. “Miranda and Jacob will brief you.”

 

“Miranda killed Wilson in cold blood. Jacob’s just a gun for hire. You expect me to trust them?” He wasn’t about to put his life in the hand of two people he hardly knew.

 

“Wilson was one of my best agents, but he was a traitor. Miranda did exactly what I expected of her. And she saved your life in more ways than one. Jacob’s a soldier, one of the best. He’s never fully trusted me, but he’s always been honest about it.” The two were capable in a fight as well. “You’ll be just fine with them, for now.”

 

“Is this a volunteer job or am I being volunteered?” He asked defiantly.

 

“You always have a choice, Shepard. If you don’t fine the evidence we’re both looking for we can part ways. But first go to Freedom’s Progress and find any clues you can.”

 

“I brought you back, its up to you to do the rest.” The Illusive Man said before tapping on something on his chair that broke the connection.

 

_-_

 

**Shepard at the Normandy after Freedom’s Progress**

 

He’d expected to find at least one survivor at the colony, but the colony was completely deserted. Except for the Quarian squad, led by Tali, he encountered. Seeing an old friend, even for a brief moment, made him feel grateful. He tried convince Tali to join him, but she refused saying that she would like to, though she had other responsibilities she needed to handle.

 

When they returned back to the Cerberus facility. Shepard spoke with the Illusive and again. The manipulative man already knew that the Collector’s were aiding the Reapers. He just wanted Shepard to confirm his suspicions. The Illusive Man revealed all that he knew about the Collectors before telling Shepard what connected the Reapers to the Collects. The biggest convincing evidence was the Omega 4 Relay. If Shepard was going to take on the excursion he needed a team he could count on. Unfortunately for him his old crew wasn’t available so he had to settle for the Illusive Man’s compiled list of Dossiers.

 

Before cutting the connection the Illusive Man recommended he’d go to the Omega base to look for a scientist named Mordin Solus and to inform him that he recruited a pilot he could trust.

 

That pilot was Joker. The wise cracking soldier was to be his pilot for whatever vessel Cerberus provided.

 

He didn’t expect that vessel to be the Normandy SR-2. A new and improved version of his old ship.

 

Looks like two things were resurrected that day.

 

He met EDI, the crew, and explored the ship before finally retreated the Captains Cabin.

 

Entering the cabin, he saw a large fish tank and another EDI interface panel. The bedroom had a plush looking bed and a lounge area with a coffee table. To the right was a bathroom and a desk area. The desk had a personal console for him to check his messages or call orders to the rest of the crew.

 

Then he saw it. A picture of Kaidan Alenko with his head turned slightly to the side, gazing at something.

 

Shepard froze and stared at the image. Feelings of hurt and sadness came to the for front again, but he didn’t relent. He pushed them back as best he could. He couldn’t break. Not yet.

 

He grabbed the chair and sat in front of the image. Shepard put his arms on his legs and clasped his hands together to bring them up to his chin in thought.

 

He couldn’t break. So he couldn’t accept his death either.

 

“Hey Kaidan.” Shepard spoke to the image in front of him.

 

“Looks like we’re going on another adventure.” Tears threatened to push out but he rubbed them away.

 

‘ _Only you’re not here.’_ He ignored the small voice in the back of his mind.

 

He didn’t notice the specter of Kaidan appear behind him grasping his shoulder.

**Notes for the Chapter:**

> Questions, comments, concerns, all welcomed.
> 
> Feel free to look for me on Tumblr
> 
> CommanderCereith

**Author's Note:**

> Kaidan is a Biotic God, just saying!!
> 
> So how was it?
> 
> Questions, comments, concerns, Kudos?
> 
> Look for me on tumblr!  
> Commander Cereith
> 
>  
> 
> :)


End file.
